Abstract

Protein-protein interactions are critical for most cellular processes; however, many
remain to be identified. Here, to comprehensively identify protein complexes in photosynthetic
organisms, we applied the recently developed approach of blue native PAGE (BN-PAGE)
coupled with LC-MS/MS to the thylakoid proteins of Arabidopsis thaliana and the whole cell proteins of whole cell proteins of Synechocystis sp. PCC 6803. We identified 245 proteins from the purified Arabidopsis thylakoid membranes and 1,458 proteins from the whole cells of Synechocystis using the method. Next, we generated protein migration profiles that were assessed
by plotting the label-free estimations of protein abundances versus migration distance
in BN-PAGE. Comparisons between the migration profiles of the major photosynthetic
complexes and their band patterns showed that the protein migration profiles were
well correlated. Thus, the protein migration profiles allowed us to estimate the molecular
size of each protein complex and to identify co-migrated proteins with the proteins
of interest by determining the protein pairs that contained peaks in the same gel
slice. Finally, we built the protein co-migration database for photosynthetic organisms
(PCoM-DB: http://pcomdb.lowtem.hokudai.ac.jp/proteins/topwebcite) to make our data publicly accessible online, which stores the analyzed data with
a user-friendly interface to compare the migration profiles of proteins of interest.
It helps users to find unidentified protein complexes in Arabidopsis thylakoids and Synechocystis cells. The accumulation of the data from the BN-PAGE coupled with LC-MS/MS should
reveal unidentified protein complexes and should aid in understanding the adaptation
and the evolution of photosynthetic organisms.